Annotation Conf. Call 2015-10-27: Difference between revisions
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:- Co-IP ; Pull down assay: | :- Co-IP ; Pull down assay: | ||
:tbx5a and kctd10 physically interact with each other. | :tbx5a and kctd10 physically interact with each other. | ||
'''Annotations:''' | |||
9 sets of annotations received. | |||
'''Analysis and points of discussion:''' (in no particular order) | |||
- Most of us annotated kct10 to heart looping/atrioventricular canal development with IMP | |||
- Use of IEP: One annotation used IEP (Inferred from Expression Pattern) as evidence code because the annotation based on altered expression of AVC marker genes (Fig 2) | |||
kctd10 atrioventricular canal development GO:0036302 IEP | |||
- “negative regulation of transcription from RNA polymerase II promoter” (GO:0000122) based on the change in gene expression assessed by in situ hybridization (Fig2). | |||
examples: | |||
kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of (Has2)|regulates_transcription_of(anf)|regulates_transcripition_of(amhc)|regulates_transcripion_of(Bmp4)|regulates_transcription_of(Notch1b) | |||
kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of: tbx2b, occurs_in myocardium, happens_during cardiac chamber morphogenesis | |||
- Is there enough evidence for the following annotations? | |||
kctd10 eye development GO:0001654 IMP kctd10 | |||
kctd10 head development GO:0060322 IMP kctd10 | |||
It is possible that the eye/head phenotype is a secondary phenotype. | |||
- The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context? | |||
Example: | |||
kctd10 endocardium development GO:0003157 IMP | |||
kctd10 endocardium morphogenesis GO:0003160 IMP | |||
kctd10 endocardium formation GO:0060214 IMP | |||
- in Figure 3: hyaluronic acid staining was performed to visualize the cardiac jelly. | |||
Annotation: | |||
kctd10 negative regulation of hyaluronan biosynthetic process GO:1900126 IMP | |||
Is there enough evidence that kctd10 is involved in hyaluronan biosynthesis? | |||
Could it be possible that the increase in staining is a secondary effect? | |||
- Fig4: injection of tbx5MO and has2MO rescue kctd10 mutant phenotype: | |||
Most of us annotated using IGI between tbx5 and kctd10, and between has2 and kctd10 heart looping/atrioventricular canal development | |||
- Should kct10 be annotated as “positive/negative regulation” of heart looping / atrioventricular canal development? | |||
- Annotation: | |||
has2 negative regulation of heart looping GO:1901208 IGI kctd10 | |||
- Fig 5: regulation of transcription : which evidence code should be used? | |||
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA | |||
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) | |||
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) | |||
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) | |||
kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b | |||
- protein binding: which evidence code should be used? | |||
examples: | |||
kct10 protein binding GO:0005515 IPI tbx5a | |||
kctd10 transcription factor binding GO:0008134 IPI tbx5a | |||
kctd10 activating transcription factor binding GO:0033613 IPI | |||
ktcd10 RNA polymerase II activating transcription factor binding GO:0001102 IDA has_direct_input Tbx5 | |||
Kctd10 transcriptional repressor activity, RNA polymerase II transcription factor binding GO:0001191 IPI tbx5a | |||
==Minutes== | ==Minutes== | ||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Revision as of 19:48, 26 October 2015
Meeting URL: https://bluejeans.com/993661940
Agenda
Annotation Consistency Exercise
Annotation consistency paper picked by ZFIN- PMID:24430697
Choice of paper-motivation: discussing the use of IGI as evidence code. When should we use IGI?
- - mutation in gene A is rescued by a mutation in gene B
- - mutation in gene A is rescued by over-expression in gene
In this paper, how do we capture
- - the repression of transcriptional activation activity of tbx5a by kctd10?
- - the information about has2
Summary of the paper (PMID:24430697) - mutants in kctd10 show heart defects (heart looping, atrioventricular canal development) Note: phenotypes determined by
- - analysis of heart morphology
- - gene expression analysis of genes known to be expressed in specific part of the heart).
[Fig 1, 2, 3]
- downregulation of tbx5a or has 2 (using MO) rescue kctd10 mutant heart phenotypes. [Fig 4]
- in vitro experiments [Fig5]:
- - luciferase reporter assay
- kctd10 inhibits tbx5 transcriptional activity
- - Co-IP ; Pull down assay:
- tbx5a and kctd10 physically interact with each other.
Annotations: 9 sets of annotations received.
Analysis and points of discussion: (in no particular order) - Most of us annotated kct10 to heart looping/atrioventricular canal development with IMP
- Use of IEP: One annotation used IEP (Inferred from Expression Pattern) as evidence code because the annotation based on altered expression of AVC marker genes (Fig 2) kctd10 atrioventricular canal development GO:0036302 IEP
- “negative regulation of transcription from RNA polymerase II promoter” (GO:0000122) based on the change in gene expression assessed by in situ hybridization (Fig2). examples: kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of (Has2)|regulates_transcription_of(anf)|regulates_transcripition_of(amhc)|regulates_transcripion_of(Bmp4)|regulates_transcription_of(Notch1b) kctd10 negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP regulates_transcription_of: tbx2b, occurs_in myocardium, happens_during cardiac chamber morphogenesis
- Is there enough evidence for the following annotations? kctd10 eye development GO:0001654 IMP kctd10 kctd10 head development GO:0060322 IMP kctd10 It is possible that the eye/head phenotype is a secondary phenotype.
- The terms including “development”, “morphogenesis”, “formation” are confusing. What is the difference? Which one should we use in this context? Example: kctd10 endocardium development GO:0003157 IMP kctd10 endocardium morphogenesis GO:0003160 IMP kctd10 endocardium formation GO:0060214 IMP
- in Figure 3: hyaluronic acid staining was performed to visualize the cardiac jelly. Annotation: kctd10 negative regulation of hyaluronan biosynthetic process GO:1900126 IMP Is there enough evidence that kctd10 is involved in hyaluronan biosynthesis? Could it be possible that the increase in staining is a secondary effect?
- Fig4: injection of tbx5MO and has2MO rescue kctd10 mutant phenotype: Most of us annotated using IGI between tbx5 and kctd10, and between has2 and kctd10 heart looping/atrioventricular canal development
- Should kct10 be annotated as “positive/negative regulation” of heart looping / atrioventricular canal development?
- Annotation: has2 negative regulation of heart looping GO:1901208 IGI kctd10
- Fig 5: regulation of transcription : which evidence code should be used?
kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a)
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a)
Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a)
kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b
- protein binding: which evidence code should be used? examples: kct10 protein binding GO:0005515 IPI tbx5a kctd10 transcription factor binding GO:0008134 IPI tbx5a kctd10 activating transcription factor binding GO:0033613 IPI ktcd10 RNA polymerase II activating transcription factor binding GO:0001102 IDA has_direct_input Tbx5 Kctd10 transcriptional repressor activity, RNA polymerase II transcription factor binding GO:0001191 IPI tbx5a